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root/gclib/gclib/GAlnExtend.h
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# Line 578 | Line 578
578   class GXBandSet:public GList<GXBand> {
579    public:
580     GXSeed* qmatch; //long match (mismatches allowed) if a very good match was extended well
581 <   GXSeed* tmatch; //terminal match to be used if there is no better alignment
581 >   GXSeed* tmatch_r; //terminal match to be used if there is no better alignment
582 >   GXSeed* tmatch_l; //terminal match to be used if there is no better alignment
583     int idxoffset; //global anti-diagonal->index offset (a_len-1)
584     //used to convert a diagonal to an index
585     //diagonal is always b_ofs-a_ofs, so the minimum value is -a_len+1
# Line 592 | Line 593
593     GXBandSet(int a_len, int b_len):GList<GXBand>(a_len+b_len-1, false, true, false) {
594        idxoffset=a_len-1;
595        qmatch=NULL;
596 <      tmatch=NULL; //terminal match to be used if everything else fails
596 >      tmatch_l=NULL; //terminal match to be used if everything else fails
597 >      tmatch_r=NULL;
598            //diag will range from -a_len+1 to b_len-1, so after adjustment
599            //by idxoffset we get a max of a_len+b_len-2
600        int bcount=a_len+b_len-1;
# Line 666 | Line 668
668   uint16 get6mer(char* p);
669   void table6mers(const char* s, int slen, GVec<uint16>* amers[]);
670  
671 < GXBandSet* collectSeeds_R(GList<GXSeed>& seeds, GXSeqData& sd); //for overlap at 3' end of seqb
671 > //GXBandSet* collectSeeds_R(GList<GXSeed>& seeds, GXSeqData& sd); //for overlap at 3' end of seqb
672  
673 < GXBandSet* collectSeeds_L(GList<GXSeed>& seeds, GXSeqData& sd); //for overlap at 5' end of seqb
673 > GXBandSet* collectSeeds(GList<GXSeed>& seeds, GXSeqData& sd); //for overlap at 5' end of seqb
674  
675   void printEditScript(GXEditScript* ed_script);
676  
# Line 731 | Line 733
733  
734    bool validate(int sl, int sr, int alnpid, int adist) {
735     int alnlen=sr-sl+1;
736 <   if (alnpid>93 && alnlen>safelen) return true;
736 >   if (alnpid>=90 && alnlen>safelen) return true;
737     sl--;sr--; //boundary is 0-based
738     int badj=0; //default boundary is 3 bases distance to end
739     int admax=1;
# Line 771 | Line 773
773   GXAlnInfo* GreedyAlign(const char* q_seq,  int q_alnstart, const char* s_seq, int s_alnstart,
774          bool editscript=false, int reward=2, int penalty=3, int xdrop=8);
775  
776 < GXAlnInfo* match_LeftEnd(GXSeqData& sd, CGreedyAlignData* gxmem=NULL, int min_pid=83);
777 < GXAlnInfo* match_RightEnd(GXSeqData& sd, CGreedyAlignData* gxmem=NULL, int min_pid=73);
776 > GXAlnInfo* match_LeftEnd(GXSeqData& sd, CGreedyAlignData* gxmem=NULL, int min_pid=90);
777 > GXAlnInfo* match_RightEnd(GXSeqData& sd, CGreedyAlignData* gxmem=NULL, int min_pid=90);
778   #endif

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